\name{plot.cna.bacom}
\alias{plot.cna.bacom}
\title{Plot DNA copy number profiles for BACOM}
\description{
'plot.cna.bacom' plots DNA copy number profiles.
}
\usage{
plot.cna.bacom(copyNumber, chrID, segMean, alpha, 
               position = 1:length(copyNumber), 
               ylim = c(-1, 6), chrToPlot=paste(1:22), 
               isPlotSegMeanBeforeCorrection = TRUE, 
               isShowLegend = TRUE, isShowAlpha = TRUE) 
}
\arguments{
\item{copyNumber}{a vector of copy number profile.}
\item{chrID}{a character vector of chromosome IDs.}
\item{segMean}{segment means.}
\item{alpha}{percentage of normal cell contamination.}
\item{position}{a vector of x-axis indices (consecutive numbers or physical locations).}
\item{ylim}{y-axis limit.}
\item{chrToPlot}{a character vector of chromosome IDs to be plotted.}
\item{isPlotSegMeanBeforeCorrection}{TRUE if to plot segment mean before correction.}
\item{isShowLegend}{TRUE if to show legend on the figure.}
\item{isShowAlpha}{TRUE if to show the value of alpha on the figure.}
}



\examples{
 plot.cna.bacom(copyNumber, chrID, segMean, alpha)
}

